              :bt1 :bt2)
         star (-> template (get-in [:nodes :ph1 :name])
                  (cljstr/includes? "star"))
+        paired (-> template (get-in [:nodes :ph1 :name])
+                 (cljstr/includes? "paired"))
         sample-names (get-exp-info eid :sample-names)
         sample-names (if repk
                        (mapcat #((get-exp-info eid :replicate-names) %)

            (keep-indexed (fn[idx itm] (when (str/substring? repname itm) idx)))
            (mapv fqzs))))))

(defn replicate-name->strain-name [eid rnm]
  ((get-exp-info eid :ncbi-sample-xref) (->> rnm (str/split #"-") first)))


                 (let [job (assoc-in phase1-job-template [:nodes :ph1 :args]
                                     (get-phase-1-args
                                      exp eid snm :repk repk
                                      :bowtie bt :star star :paired paired))
                       cfg (-> job
                               (pg/config-pgm-graph-nodes get-toolinfo nil nil)
                               pg/config-pgm-graph)]
